Contacts of the strand formed by residues 273 - 279 (chain G) in PDB entry 5DST
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with CYS 273 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297B GLN* 4.5 0.7 - - - -
353B GLU* 3.1 35.4 - - - +
355B TYR* 4.0 0.2 - - - -
222G TYR* 3.3 6.8 - - - -
223G VAL* 3.0 34.2 + - + +
272G ALA* 1.3 76.2 - - - +
274G LEU* 1.3 72.0 + - - +
275G ILE* 3.5 0.8 + - - -
294G PHE* 3.4 29.8 - - - -
295G CYS 3.3 22.7 - - - +
296G LEU* 3.8 9.0 - - + -
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Residues in contact with LEU 274 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B GLN* 5.2 1.2 + - - -
350B ARG 5.4 2.0 - - - +
351B GLY* 3.8 33.9 + - - +
352B GLU* 4.7 5.8 - - + +
353B GLU* 4.4 8.4 + - - +
220G ALA* 3.8 17.9 - - + -
221G LEU 3.7 13.5 - - - +
222G TYR* 3.5 35.6 - - + +
272G ALA 4.4 0.2 + - - -
273G CYS* 1.3 79.9 - - - +
275G ILE* 1.3 61.6 + - - +
276G LYS 3.9 14.4 - - - +
277G GLU* 3.9 29.2 - - + +
293G ALA 4.5 3.3 - - - +
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Residues in contact with ILE 275 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221G LEU* 2.9 48.0 + - + +
222G TYR* 4.3 4.5 - - - +
223G VAL* 3.6 33.4 - - + -
273G CYS* 3.9 0.4 - - - +
274G LEU* 1.3 79.5 - - - +
276G LYS* 1.3 64.6 + - - +
290G PHE* 3.8 6.7 - - + -
292G SER* 2.5 35.5 + - - +
293G ALA 4.1 4.5 - - - +
294G PHE* 3.9 17.7 - - + -
309G THR* 4.7 2.0 - - + -
358G ILE* 3.9 35.0 - - + -
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Residues in contact with LYS 276 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191G LEU* 5.2 0.2 - - - +
192G PHE* 3.8 23.6 - - + -
219G ALA 4.1 0.3 - - - +
220G ALA* 3.3 4.3 - - - -
221G LEU* 2.8 44.6 + - + +
274G LEU* 3.8 5.3 - - - +
275G ILE* 1.3 83.5 - - - +
277G GLU* 1.3 77.0 + - - +
278G VAL* 4.2 8.3 - - + +
283G VAL* 5.8 3.1 - - - -
287G GLU* 2.8 37.7 + - - +
288G LEU* 4.8 6.7 - - - -
290G PHE* 4.0 33.9 - - + +
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Residues in contact with GLU 277 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B ARG* 3.0 43.3 + - - -
350B ARG 5.4 2.3 - - - +
352B GLU* 4.9 2.1 - - - +
381B GLN* 4.2 9.5 - - - +
218G ARG* 3.3 35.0 + - - +
219G ALA 3.7 3.6 - - - +
220G ALA* 4.6 1.8 - - + +
274G LEU* 3.9 25.7 - - + +
276G LYS* 1.3 84.7 - - - +
278G VAL* 1.3 72.1 + - - +
279G ASP 4.2 1.0 + - - +
283G VAL* 4.7 3.5 - - - +
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Residues in contact with VAL 278 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186G TRP* 5.2 0.9 - - + -
191G LEU* 4.8 0.7 - - + -
192G PHE* 3.9 30.7 - - + -
197G LEU* 4.2 11.2 - - + -
218G ARG* 3.4 11.8 - - - +
219G ALA* 2.9 44.0 + - + +
276G LYS* 4.2 11.4 - - + +
277G GLU* 1.3 84.4 - - - +
279G ASP* 1.3 59.1 + - - +
280G ILE* 3.5 17.4 + - + -
283G VAL* 3.8 30.3 - - + -
288G LEU* 4.9 2.5 - - + -
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Residues in contact with ASP 279 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B GLN* 5.3 9.2 - - - +
217G ASP 3.9 5.1 - - - +
218G ARG* 5.1 6.7 - - + +
277G GLU* 4.2 1.6 + - - +
278G VAL* 1.3 71.7 - - - +
280G ILE* 1.3 64.8 + - - +
281G TYR* 3.4 28.5 - - - +
282G THR* 2.9 42.8 + - - +
283G VAL* 3.0 18.1 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il